Figure 4.

Strain Persistence, Strain Replacement Events, and Strain Heterogeneity

(A) Map of the strain dynamics in longitudinal infant stool (FE) samples for selected species (for full map, see Figure S6). The tongue dorsum (TD) column shows the species for which at least one of the strains found in stool was also present on the tongue dorsum. Blue circles represent the first strain of the species identified in the infant, whereas orange and green circles denote the second and third longitudinally identified strain, respectively. Empty circles refer to species for which strain profiling was not possible in the specific sample. Missing samples and samples lacking the species are not reported. The total number of infant replacement events observed in each species is shown in parentheses.

(B) Mean percentages of polymorphic sites and average frequency of the dominant alleles in polymorphic sites for each body site and time point (“M” indicates maternal samples). Color coding is as per Figure 1. p values are reported in Table S4. Error bars refer to 95% confidence intervals.